RLagoon

RLagoon

R client for lagoon.

This package implements functions to ingest and retrieve data from lagoon. It also implements a DBI driver for the Lagoon server and a dplyr backend which employs the DBI driver.

Install RLagoon with

$ R --slave -e "install.packages(c('dbplyr', dplyr', 'jsonlite', 'httr'), repos='http://cran.us.r-project.org')"
$ R --slave -e "install.packages('RLagoon', repos=NULL, type='sources')"

Querying for data

This is how one connects to Lagoon in R using the dplyr backend:

require(RLagoon)
dbConn <- src_lagoon(host = "localhost", port = "22089")

localhost and port are replaced by the lagoon REST server.

Then dplyr can be used to query tables.

require(dplyr)
t <- tbl(dbConn, "users")

RLagoon offers some facilities to write queries using json operators. The list of json operators is available in the PostgreSQL documentation. See the documentation of RLagoon::sql_translate_env.LagoonConnection for details.

This example lists all users whose name is "John", where the users are assumed to reside in a table with a column called data of type json or jsonb.

collect(filter(t, data %->>% "name" == "John"))

The script ../examples/ingest_json_demo.sh contains step-by-step instructions to try the json operators.

Importing data

This is an example of using ingest.

ingest(owner="mary", json_path='{ "response" : { "docs" : [_] } }'
      , source_name="genenames/genes_with_protein_product",
      , source_path="gene_with_protein_product.json"
      )

The example uses environment variables to reach the database (PGHOST, PGUSER, etc, as described in the ingest documentation).

A database configuration can be created with createConfig and set as global default with setDefaultConfig. Also, the function ingest can take an optional configuration parameter config=someConfiguration to use instead of the global one.

To see the json type of a table without importing it, one can use:

infer_json_type("gene_with_protein_product.json")

See ../examples/ingest_json_demo.sh for a step-by-step example of using ingest from R.

And lastly we have operations to list users, tables and columns.

getUsers()
getTableNames()
getColumns(someTableName)